bims-auttor 2020-07-12 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2020–07–12
38 papers selected by
Viktor Korolchuk, Newcastle University

Regulation and repurposing of nutrient sensing and autophagy in innate immunity.
Aging is associated with a decline in Atg9b-mediated autophagosome formation and appearance of enlarged mitochondria in the heart.
USP30 sets a trigger threshold for PINK1-PARKIN amplification of mitochondrial ubiquitylation.
Aster-C coordinates with COP I vesicles to regulate lysosomal trafficking and activation of mTORC1.
Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Interferon-independent STING signaling promotes resistance to HSV-1 in vivo.
Lysosomal recycling of amino acids affects ER quality control.
RNF126-Mediated Reubiquitination Is Required for Proteasomal Degradation of p97-Extracted Membrane Proteins.
Mitophagy regulates integrity of mitochondria at synapses and is critical for synaptic maintenance.
Endoplasmic Reticulum-Mitochondria Contact Sites and Neurodegeneration.
Stress Induces Dynamic, Cytotoxicity-Antagonizing TDP-43 Nuclear Bodies via Paraspeckle LncRNA NEAT1-Mediated Liquid-Liquid Phase Separation.
Small Trafficking Inhibitor Retro-2 Disrupts the Microtubule-Dependent Trafficking of Autophagic Vacuoles.
GSK-3β inhibition by curcumin mitigates amyloidogenesis via TFEB activation and anti-oxidative Activity in human neuroblastoma cells.
Trehalose alleviates apoptosis by protecting the autophagy-lysosomal system in alveolar macrophages during human silicosis.
Glucosylation by the Legionella Effector SetA Promotes the Nuclear Localization of the Transcription Factor TFEB.
p18/Lamtor1-mTORC1 Signaling Controls Development of Mucin-producing Goblet Cells in the Intestine.
Canonical and Noncanonical Autophagy as Potential Targets for COVID-19.
Death-associated Protein Kinase 1 Phosphorylates α-Synuclein at Ser129 and Exacerbates Rotenone-induced Toxic Aggregation of α-Synuclein in Dopaminergic SH-SY5Y Cells.
Proteoglycan-driven Autophagy: A Nutrient-independent Mechanism to Control Intracellular Catabolism.
Lipophagy: Molecular Mechanisms and Implications in Metabolic Disorders.
Lipid excess affects chaperone-mediated autophagy in hypothalamus.
Autophagy as a modulator of cell death machinery.
An update on cellular and molecular determinants of Parkinson's disease with emphasis on the role of the retromer complex.
Parkin, an E3 Ubiquitin Ligase, Plays an Essential Role in Mitochondrial Quality Control in Parkinson's Disease.
Rapamycin Alleviates Hypertriglyceridemia-Related Acute Pancreatitis via Restoring Autophagy Flux and Inhibiting Endoplasmic Reticulum Stress.
Exogenous supplement of glucagon like peptide-1 protects the heart against aortic banding induced myocardial fibrosis and dysfunction through inhibiting mTOR/p70S6K signaling and promoting autophagy.
Lipoic acid rejuvenates aged intestinal stem cells by preventing age-associated endosome reduction.
Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces.
Real-time in vivo imaging of extracellular ATP in the brain with a hybrid-type fluorescent sensor.
Mitochondrial Fatty Acids and Neurodegenerative Disorders.
mTORC1 and mTORC2 expression in inner retinal neurons and glial cells.
Dopaminergic neurodegeneration induced by Parkinson's disease-linked G2019S LRRK2 is dependent on kinase and GTPase activity.
Experimental Approaches in Delineating mTOR Signaling.
Autophagy in the crosstalk between tumor and microenvironment.
Overexpression of ATG4a promotes autophagy and proliferation, and inhibits apoptosis in lens epithelial cells via the AMPK and Akt pathways.
ATM-deficient neural precursors develop senescence phenotype with disturbances in autophagy.
Molecular Mechanisms of Lysosome and Nucleus Communication.
Metabolic pathways in context: mTOR signalling in the retina and optic nerve.

Autophagy. 2020 Jul 05. 1-21

Regulation and repurposing of nutrient sensing and autophagy in innate immunity.

Julia Sanchez-Garrido, Avinash R Shenoy.

  Nutrients not only act as building blocks but also as signaling molecules. Nutrient-availability promotes cell growth and proliferation and suppresses catabolic processes, such as macroautophagy/autophagy. These effects are mediated by checkpoint kinases such as MTOR (mechanistic target of rapamycin kinase), which is activated by amino acids and growth factors, and AMP-activated protein kinase (AMPK), which is activated by low levels of glucose or ATP. These kinases have wide-ranging activities that can be co-opted by immune cells upon exposure to danger signals, cytokines or pathogens. Here, we discuss recent insight into the regulation and repurposing of nutrient-sensing responses by the innate immune system during infection. Moreover, we examine how natural mutations and pathogen-mediated interventions can alter the balance between anabolic and autophagic pathways leading to a breakdown in tissue homeostasis and/or host defense.
ABBREVIATIONS: AKT1/PKB: AKT serine/threonine kinase 1; ATG: autophagy related; BECN1: beclin 1; CGAS: cyclic GMP-AMP synthase; EIF2AK4/GCN2: eukaryotic translation initiation factor 2 alpha kinase 4; ER: endoplasmic reticulum; FFAR: free fatty acid receptor; GABARAP: GABA type A receptor-associated protein; IFN: interferon; IL: interleukin; LAP: LC3-associated phagocytosis; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK: mitogen-activated protein kinase; MTOR: mechanistic target of rapamycin kinase; NLR: NOD (nucleotide-binding oligomerization domain) and leucine-rich repeat containing proteins; PI3K, phosphoinositide 3-kinase; PRR: pattern-recognition receptor; PtdIns3K: phosphatidylinositol 3-kinase; RALB: RAS like proto-oncogene B; RHEB: Ras homolog, MTORC1 binding; RIPK1: receptor interacting serine/threonine kinase 1; RRAG: Ras related GTP binding; SQSTM1/p62: sequestosome 1; STING1/TMEM173: stimulator of interferon response cGAMP interactor 1; STK11/LKB1: serine/threonine kinase 11; TBK1: TANK binding kinase 1; TLR: toll like receptor; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; TRIM: tripartite motif protein; ULK1: unc-51 like autophagy activating kinase 1; V-ATPase: vacuolar-type H+-proton-translocating ATPase.

Keywords:  AMPK; LC3-associated phagocytosis; MTOR; immunity; microbial pathogenesis; unconventional secretion

DOI:  https://doi.org/10.1080/15548627.2020.1783119
Aging Cell. 2020 Jul 06. e13187

Aging is associated with a decline in Atg9b-mediated autophagosome formation and appearance of enlarged mitochondria in the heart.

Wenjing Liang, Alexandra G Moyzis, Mark A Lampert, Rachel Y Diao, Rita H Najor, Åsa B Gustafsson.

  Advancing age is a major risk factor for developing heart disease, and the biological processes contributing to aging are currently under intense investigation. Autophagy is an important cellular quality control mechanism that is reduced in tissues with age but the molecular mechanisms underlying the age-associated defects in autophagy remain poorly characterized. Here, we have investigated how the autophagic process is altered in aged mouse hearts. We report that autophagic activity is reduced in aged hearts due to a reduction in autophagosome formation. Gene expression profile analysis to evaluate changes in autophagy regulators uncovered a reduction in Atg9b transcript and protein levels. Atg9 proteins are critical in delivering membrane to the growing autophagosome, and siRNA knockdown of Atg9b in cells confirmed a reduction in autophagosome formation. Autophagy is also the main pathway involved in eliminating dysfunctional mitochondria via a process known as mitophagy. The E3 ubiquitin ligase Parkin plays a key role in labeling mitochondria for mitophagy. We also found increased levels of Parkin-positive mitochondria in the aged hearts, an indication that they have been labeled for mitophagy. In contrast, Nrf1, a major transcriptional regulator of mitochondrial biogenesis, was significantly reduced in aged hearts. Additionally, our data showed reduced Drp1-mediated mitochondrial fission and formation of enlarged mitochondria in the aged heart. Overall, our findings suggest that cardiac aging is associated with reduced autophagosome number, decreased mitochondrial turnover, and formation of megamitochondria.

Keywords:  Atg9; Parkin; aging; autophagy; heart; mitochondria; mitophagy

DOI:  https://doi.org/10.1111/acel.13187
Life Sci Alliance. 2020 Aug;pii: e202000768. [Epub ahead of print]3(8):

USP30 sets a trigger threshold for PINK1-PARKIN amplification of mitochondrial ubiquitylation.

Emma V Rusilowicz-Jones, Jane Jardine, Andreas Kallinos, Adan Pinto-Fernandez, Franziska Guenther, Mariacarmela Giurrandino, Francesco G Barone, Katy McCarron, Christopher J Burke, Alejandro Murad, Aitor Martinez, Elena Marcassa, Malte Gersch, Alexandre J Buckmelter, Katherine J Kayser-Bricker, Frederic Lamoliatte, Akshada Gajbhiye, Simon Davis, Hannah C Scott, Emma Murphy, Katherine England, Heather Mortiboys, David Komander, Matthias Trost, Benedikt M Kessler, Stephanos Ioannidis, Michael K Ahlijanian, Sylvie Urbé, Michael J Clague.

The mitochondrial deubiquitylase USP30 negatively regulates the selective autophagy of damaged mitochondria. We present the characterisation of an N-cyano pyrrolidine compound, FT3967385, with high selectivity for USP30. We demonstrate that ubiquitylation of TOM20, a component of the outer mitochondrial membrane import machinery, represents a robust biomarker for both USP30 loss and inhibition. A proteomics analysis, on a SHSY5Y neuroblastoma cell line model, directly compares the effects of genetic loss of USP30 with chemical inhibition. We have thereby identified a subset of ubiquitylation events consequent to mitochondrial depolarisation that are USP30 sensitive. Within responsive elements of the ubiquitylome, several components of the outer mitochondrial membrane transport (TOM) complex are prominent. Thus, our data support a model whereby USP30 can regulate the availability of ubiquitin at the specific site of mitochondrial PINK1 accumulation following membrane depolarisation. USP30 deubiquitylation of TOM complex components dampens the trigger for the Parkin-dependent amplification of mitochondrial ubiquitylation leading to mitophagy. Accordingly, PINK1 generation of phospho-Ser65 ubiquitin proceeds more rapidly in cells either lacking USP30 or subject to USP30 inhibition.

DOI: https://doi.org/10.26508/lsa.202000768
EMBO Rep. 2020 Jul 09. e49898

Aster-C coordinates with COP I vesicles to regulate lysosomal trafficking and activation of mTORC1.

Jun Zhang, John-Paul Andersen, Haoran Sun, Xuyun Liu, Nahum Sonenberg, Jia Nie, Yuguang Shi.

  Nutrient sensing by the mTOR complex 1 (mTORC1) requires its translocation to the lysosomal membrane. Upon amino acids removal, mTORC1 becomes cytosolic and inactive, yet its precise subcellular localization and the mechanism of inhibition remain elusive. Here, we identified Aster-C as a negative regulator of mTORC1 signaling. Aster-C earmarked a special rough ER subdomain where it sequestered mTOR together with the GATOR2 complex to prevent mTORC1 activation during nutrient starvation. Amino acids stimulated rapid disassociation of mTORC1 from Aster-C concurrently with assembly of COP I vesicles which escorted mTORC1 to the lysosomal membrane. Consequently, ablation of Aster-C led to spontaneous activation of mTORC1 and dissociation of TSC2 from lysosomes, whereas inhibition of COP I vesicle biogenesis or actin dynamics prevented mTORC1 activation. Together, these findings identified Aster-C as a missing link between lysosomal trafficking and mTORC1 activation by revealing an unexpected role of COP I vesicles in mTORC1 signaling.

Keywords:  ARF1; COP I; GRAMD1C; lysosomes; mTORC1

DOI:  https://doi.org/10.15252/embr.201949898
Proc Natl Acad Sci U S A. 2020 Jul 06. pii: 202008030. [Epub ahead of print]

Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.

Hersh K Bhargava, Keisuke Tabata, Jordan M Byck, Maho Hamasaki, Daniel P Farrell, Ivan Anishchenko, Frank DiMaio, Young Jun Im, Tamotsu Yoshimori, James H Hurley.

  Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7-GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab-effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.

Keywords:  Rab GTPase; autophagy; crystal structure

DOI:  https://doi.org/10.1073/pnas.2008030117
Nat Commun. 2020 Jul 07. 11(1): 3382

Interferon-independent STING signaling promotes resistance to HSV-1 in vivo.

Lívia H Yamashiro, Stephen C Wilson, Huntly M Morrison, Vasiliki Karalis, Jing-Yi J Chung, Katherine J Chen, Helen S Bateup, Moriah L Szpara, Angus Y Lee, Jeffery S Cox, Russell E Vance.

The Stimulator of Interferon Genes (STING) pathway initiates potent immune responses upon recognition of DNA. To initiate signaling, serine 365 (S365) in the C-terminal tail (CTT) of STING is phosphorylated, leading to induction of type I interferons (IFNs). Additionally, evolutionary conserved responses such as autophagy also occur downstream of STING, but their relative importance during in vivo infections remains unclear. Here we report that mice harboring a serine 365-to-alanine (S365A) mutation in STING are unexpectedly resistant to Herpes Simplex Virus (HSV)-1, despite lacking STING-induced type I IFN responses. By contrast, resistance to HSV-1 is abolished in mice lacking the STING CTT, suggesting that the STING CTT initiates protective responses against HSV-1, independently of type I IFNs. Interestingly, we find that STING-induced autophagy is a CTT- and TBK1-dependent but IRF3-independent process that is conserved in the STING S365A mice. Thus, interferon-independent functions of STING mediate STING-dependent antiviral responses in vivo.

DOI: https://doi.org/10.1038/s41467-020-17156-x
Sci Adv. 2020 Jun;6(26): eaaz9805

Lysosomal recycling of amino acids affects ER quality control.

Ryo Higuchi-Sanabria, Koning Shen, Naame Kelet, Phillip A Frankino, Jenni Durieux, Raz Bar-Ziv, Cierra N Sing, Enrique J Garcia, Stefan Homentcovschi, Melissa Sanchez, Rui Wu, Sarah U Tronnes, Larry Joe, Brant Webster, Alex Ahilon-Jeronimo, Samira Monshietehadi, Sofia Dallarda, Corinne Pender, Liza A Pon, Roberto Zoncu, Andrew Dillin.

Recent work has highlighted the fact that lysosomes are a critical signaling hub of metabolic processes, providing fundamental building blocks crucial for anabolic functions. How lysosomal functions affect other cellular compartments is not fully understood. Here, we find that lysosomal recycling of the amino acids lysine and arginine is essential for proper ER quality control through the UPRER. Specifically, loss of the lysine and arginine amino acid transporter LAAT-1 results in increased sensitivity to proteotoxic stress in the ER and decreased animal physiology. We find that these LAAT-1-dependent effects are linked to glycine metabolism and transport and that the loss of function of the glycine transporter SKAT-1 also increases sensitivity to ER stress. Direct lysine and arginine supplementation, or glycine supplementation alone, can ameliorate increased ER stress sensitivity found in laat-1 mutants. These data implicate a crucial role in recycling lysine, arginine, and glycine in communication between the lysosome and ER.

DOI: https://doi.org/10.1126/sciadv.aaz9805
Mol Cell. 2020 Jun 30. pii: S1097-2765(20)30425-1. [Epub ahead of print]

RNF126-Mediated Reubiquitination Is Required for Proteasomal Degradation of p97-Extracted Membrane Proteins.

Xianyan Hu, Linhan Wang, Yuancai Wang, Jia Ji, Jiqiang Li, Zhiyuan Wang, Congcong Li, Yaoyang Zhang, Zai-Rong Zhang.

  Valosin-containing protein (VCP)/p97 is an AAA-ATPase that extracts polyubiquitinated substrates from multimeric macromolecular complexes and biological membranes for proteasomal degradation. During p97-mediated extraction, the substrate is largely deubiquitinated as it is threaded through the p97 central pore. How p97-extracted substrates are targeted to the proteasome with few or no ubiquitins is unknown. Here, we report that p97-extracted membrane proteins undergo a second round of ubiquitination catalyzed by the cytosolic ubiquitin ligase RNF126. RNF126 interacts with transmembrane-domain-specific chaperone BAG6, which captures p97-liberated substrates. RNF126 depletion in cells diminishes the ubiquitination of extracted membrane proteins, slows down their turnover, and dramatically stabilizes otherwise transient intermediates in the cytosol. We reconstitute the reubiquitination of a p97-extracted, misfolded multispanning membrane protein with purified factors. Our results demonstrate that p97-extracted substrates need to rapidly engage ubiquitin ligase-chaperone pairs that rebuild the ubiquitin signal for proteasome targeting to prevent harmful accumulation of unfolded intermediates.

Keywords:  RNF126; VCP; endoplasmic reticulum-associated degradation; membrane protein; p97/valosin-containing protein; proteasome; ubiquitination

DOI:  https://doi.org/10.1016/j.molcel.2020.06.023
EMBO Rep. 2020 Jul 06. e201949801

Mitophagy regulates integrity of mitochondria at synapses and is critical for synaptic maintenance.

Sinsuk Han, Yu Young Jeong, Preethi Sheshadri, Xiao Su, Qian Cai.

  Synaptic mitochondria are particularly vulnerable to physiological insults, and defects in synaptic mitochondria are linked to early pathophysiology of Alzheimer's disease (AD). Mitophagy, a cargo-specific autophagy for elimination of dysfunctional mitochondria, constitutes a key quality control mechanism. However, how mitophagy ensures synaptic mitochondrial integrity remains largely unknown. Here, we reveal Rheb and Snapin as key players regulating mitochondrial homeostasis at synapses. Rheb initiates mitophagy to target damaged mitochondria for autophagy, whereas dynein-Snapin-mediated retrograde transport promotes clearance of mitophagosomes from synaptic terminals. We demonstrate that synaptic accumulation of mitophagosomes is a feature in AD-related mutant hAPP mouse brains, which is attributed to increased mitophagy initiation coupled with impaired removal of mitophagosomes from AD synapses due to defective retrograde transport. Furthermore, while deficiency in dynein-Snapin-mediated retrograde transport recapitulates synaptic mitophagy stress and induces synaptic degeneration, elevated Snapin expression attenuates mitochondrial defects and ameliorates synapse loss in AD mouse brains. Taken together, our study provides new insights into mitophagy regulation of synaptic mitochondrial integrity, establishing a foundation for mitigating AD-associated mitochondria deficits and synaptic damage through mitophagy enhancement.

Keywords:  Alzheimer's; mitophagosome; retrograde transport; synaptic mitochondrial deficits; synaptic mitophagy

DOI:  https://doi.org/10.15252/embr.201949801
Front Cell Dev Biol. 2020 ;8 428

Endoplasmic Reticulum-Mitochondria Contact Sites and Neurodegeneration.

Lingna Xu, Xi Wang, Chao Tong.

  Endoplasmic reticulum-mitochondria contact sites (ERMCSs) are dynamic contact regions with a distance of 10-30 nm between the endoplasmic reticulum and mitochondria. Endoplasmic reticulum-mitochondria contact sites regulate various biological processes, including lipid transfer, calcium homeostasis, autophagy, and mitochondrial dynamics. The dysfunction of ERMCS is closely associated with various neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis. In this review, we will summarize the current knowledge of the components and organization of ERMCSs, the methods for monitoring ERMCSs, and the physiological functions of ERMCSs in different model systems. Additionally, we will emphasize the current understanding of the malfunction of ERMCSs and their potential roles in neurodegenerative diseases.

Keywords:  autophagy; contact sites; endoplasmic reticulum; mitochdonrion; neurodegeneration

DOI:  https://doi.org/10.3389/fcell.2020.00428
Mol Cell. 2020 Jul 03. pii: S1097-2765(20)30421-4. [Epub ahead of print]

Stress Induces Dynamic, Cytotoxicity-Antagonizing TDP-43 Nuclear Bodies via Paraspeckle LncRNA NEAT1-Mediated Liquid-Liquid Phase Separation.

Chen Wang, Yongjia Duan, Gang Duan, Qiangqiang Wang, Kai Zhang, Xue Deng, Beituo Qian, Jinge Gu, Zhiwei Ma, Shuang Zhang, Lin Guo, Cong Liu, Yanshan Fang.

  Despite the prominent role of TDP-43 in neurodegeneration, its physiological and pathological functions are not fully understood. Here, we report an unexpected role of TDP-43 in the formation of dynamic, reversible, liquid droplet-like nuclear bodies (NBs) in response to stress. Formation of NBs alleviates TDP-43-mediated cytotoxicity in mammalian cells and fly neurons. Super-resolution microscopy reveals distinct functions of the two RRMs in TDP-43 NB formation. TDP-43 NBs are partially colocalized with nuclear paraspeckles, whose scaffolding lncRNA NEAT1 is dramatically upregulated in stressed neurons. Moreover, increase of NEAT1 promotes TDP-43 liquid-liquid phase separation (LLPS) in vitro. Finally, we discover that the ALS-associated mutation D169G impairs the NEAT1-mediated TDP-43 LLPS and NB assembly, causing excessive cytoplasmic translocation of TDP-43 to form stress granules, which become phosphorylated TDP-43 cytoplasmic foci upon prolonged stress. Together, our findings suggest a stress-mitigating role and mechanism of TDP-43 NBs, whose dysfunction may be involved in ALS pathogenesis.

Keywords:  ALS; TDP-43; lncRNA NEAT1; nuclear body; paraspeckle; phase separation; stress granules

DOI:  https://doi.org/10.1016/j.molcel.2020.06.019
Front Cell Dev Biol. 2020 ;8 464

Small Trafficking Inhibitor Retro-2 Disrupts the Microtubule-Dependent Trafficking of Autophagic Vacuoles.

Valérie Nicolas, Vanessa Lievin-Le Moal.

  Autophagy is a catabolic recycling process by which a cell degrades its own constituents to contribute to cell homeostasis or survival. We report that the small trafficking inhibitor Retro-2 impairs microtubule-dependent vacuolar trafficking in autophagy. Retro-2 induced autophagy and promoted the dramatic cytoplasmic accumulation of large autophagosomes. Moreover, Retro-2 decreased the spreading of autophagosomes within the cytoplasm of nutrient-starved cells. In addition, Retro-2 abolished autolysosomes formation. We show that these effects arise from hitherto unsuspected disassembly activity of the small molecule on the cellular microtubule network, which is known to act as a key regulator of vacuolar trafficking of the autophagy pathway.

Keywords:  autolysosome; autophagosome; autophagy; microtubules; nutrient starvation; trafficking inhibitor Retro-2; vacuolar trafficking

DOI:  https://doi.org/10.3389/fcell.2020.00464
Free Radic Res. 2020 Jul 06. 1-39

GSK-3β inhibition by curcumin mitigates amyloidogenesis via TFEB activation and anti-oxidative Activity in human neuroblastoma cells.

Hyun-Chul Song, Yubing Chen, Yingqing Chen, Jeongmin Park, Min Zheng, Young-Joon Surh, Uh-Hyun Kim, Jeong Woo Park, Rina Yu, Hun Taeg Chung, Yeonsoo Joe.

  The translocation of transcription factor EB (TFEB) to the nucleus plays a pivotal role in the regulation of basic cellular processes, such as lysosome biogenesis and autophagy. Autophagy is an intracellular degradation system that delivers cytoplasmic constituents to the lysosome, which is important in maintaining cellular homeostasis during environmental stress. Furthermore, oxidative stress is a critical cause for the progression of neurodegenerative diseases. Curcumin has anti-oxidative and anti-inflammatory activities, and is expected to have potential therapeutic effects in various diseases. In this study, we demonstrated that curcumin regulated TFEB export signaling via inhibition of glycogen synthase kinase-3β (GSK-3β); GSK-3β was inactivated by curcumin, leading to reduced phosphorylation of TFEB. We further showed that H2O2-induced oxidative stress was reduced by curcumin via the Nrf2/HO-1 pathway in human neuroblastoma cells. In addition, we showed that curcumin induced the degradation of amyloidogenic proteins, including amyloid-β precursor protein and α-synuclein, through the TFEB-autophagy/lysosomal pathway. In conclusion, curcumin regulates autophagy by controlling TFEB through the inhibition of GSK-3β, and increases antioxidant gene expression in human neuroblastoma cells. These results contribute to the development of novel cellular therapies for neurodegenerative diseases.

Keywords:  Alzheimer's disease; Parkinson's disease; amyloid-β precursor protein (APP); autophagy; curcumin; glycogen synthase kinase 3β; human neuroblastoma cells; neurodegenerative disease; reactive oxygen species; transcription factor EB; α-synuclein (α-syn)

DOI:  https://doi.org/10.1080/10715762.2020.1791843
Life Sci. 2020 Jul 01. pii: S0024-3205(20)30793-1. [Epub ahead of print] 118043

Trehalose alleviates apoptosis by protecting the autophagy-lysosomal system in alveolar macrophages during human silicosis.

Shiyi Tan, Shang Yang, Gang Chen, Li Zhu, Zhiqian Sun, Shi Chen.

   BACKGROUND: Alveolar macrophages (AMs) are the primary targets of silicosis. Blockade of autophagy may aggravate the apoptosis of AMs. Trehalose (Tre), a transcription factor EB (TFEB) activator, may impact the autophagy-lysosomal system in AMs during silicosis. However, the mechanism by which Tre acts upon AMs in silicosis is unknown.
METHODS: We collected AMs from twenty male workers exposed to silica and divided them into observer and silicosis patient groups. AMs from the two groups were then exposed to Tre. Western blot was used to measure the expression of autophagy-associated proteins. Lysosomal-associated membrane protein 1 (LAMP1) expression was observed using immunofluorescence and western blot. Apoptosis of the AMs was detected by TUNEL assay and western blot.
RESULTS: Tre induced localization of TFEB to the nucleus in the AMs of both groups. After Tre exposure, LAMP1 levels increased and LC3 levels decreased in the AMs of both groups, suggesting that Tre may increase the function of the autophagy-lysosomal system. The LC3-II/I ratio in the Tre-exposed AMs was lower than in the AMs not exposed to Tre. The LC3-II/I ratio in AMs subjected to Tre plus Bafilomycin (Baf) was higher than the ratio in cells exposed to Tre or Baf individually. Additionally, p62 levels decreased after Tre stimulation in the AMs of both groups. This indicates that Tre may accelerate the process of autophagic degradation. We also found decreased levels of cleaved caspase-3 after Tre treatment in the AMs of both groups. However, p-mTOR (Ser2448) and p-mTOR (Ser2481) levels did not change significantly after Tre treatment, suggesting that the mTOR signaling pathway was not affected by Tre treatment.
CONCLUSION: Our findings suggest that the restoration of autophagy-lysosomal function by Tre may be a potential protective strategy against silicosis.

Keywords:  Alveolar macrophages; Apoptosis; Autophagic degradation; Autophagy; Silicosis; Trehalose

DOI:  https://doi.org/10.1016/j.lfs.2020.118043
iScience. 2020 Jun 20. pii: S2589-0042(20)30487-9. [Epub ahead of print]23(7): 101300

Glucosylation by the Legionella Effector SetA Promotes the Nuclear Localization of the Transcription Factor TFEB.

Wendy H J Beck, Dongsung Kim, Jishnu Das, Haiyuan Yu, Marcus B Smolka, Yuxin Mao.

  Legionella pneumophila is an intracellular pathogen that requires nutrients from the host for its replication. It has been shown that replicating L. pneumophila prefers amino acids as main sources of carbon and energy. The homeostasis of amino acids in eukaryotic cells is regulated by the transcription factor EB (TFEB), which translocates into the nucleus and activates genes for autophagy and lysosomal biogenesis. Here we show that the Legionella effector SetA causes a robust nuclear translocation of TFEB when exogenously expressed in mammalian cells and that the translocation is dependent on the glucosyltransferase activity of SetA. We further show that SetA directly glucosylates TFEB at multiple sites. Our findings of TFEB glucosylation by SetA may suggest an alternative strategy for exploiting host nutrients in addition to the control of host mTORC1 signaling by L. pneumophila. Our results provide further insight into the molecular mechanism of the delicate TFEB nuclear shuttling.

Keywords:  Microbiology; Molecular Biology

DOI:  https://doi.org/10.1016/j.isci.2020.101300
Cell Struct Funct. 2020 ;45(2): 93-105

p18/Lamtor1-mTORC1 Signaling Controls Development of Mucin-producing Goblet Cells in the Intestine.

Shizuka Ito, Shigeyuki Nada, Daisuke Yamazaki, Tetsuya Kimura, Kentaro Kajiwara, Hiroaki Miki, Masato Okada.

  Mechanistic target of rapamycin complex 1 (mTORC1) plays a pivotal role in controlling cell growth and metabolism in response to nutrients and growth factors. The activity of mTORC1 is dually regulated by amino acids and growth factor signaling, and amino acid-dependent mTORC1 activity is regulated by mTORC1 interaction with the Ragulator-Rag GTPase complex, which is localized to the surface of lysosomes via a membrane-anchored protein, p18/Lamtor1. However, the physiological function of p18-Ragulator-dependent mTORC1 signaling remains elusive. The present study evaluated the function of p18-mediated mTORC1 signaling in the intestinal epithelia using p18 conditional knockout mice. In p18 knockout colonic crypts, mTORC1 was delocalized from lysosomes, and in vivo mTORC1 activity was markedly decreased. Histologically, p18 knockout crypts exhibited significantly increased proliferating cells and dramatically decreased mucin-producing goblet cells, while overall crypt architecture and enteroendocrine cell differentiation were unaffected. Furthermore, p18 knockout crypts normally expressed transcription factors implicated in crypt differentiation, such as Cdx2 and Klf4, indicating that p18 ablation did not affect the genetic program of cell differentiation. Analysis of colon crypt organoid cultures revealed that both p18 ablation and rapamycin treatment robustly suppressed development of mucin-producing goblet cells. Hence, p18-mediated mTORC1 signaling could promote the anabolic metabolism required for robust mucin production in goblet cells to protect the intestinal epithelia from various external stressors.Key words: mTORC1, p18/lamtor1, intestinal epithelium, goblet cells, mucin.

Keywords:  goblet cells; intestinal epithelium; mTORC1; mucin; p18/lamtor1

DOI:  https://doi.org/10.1247/csf.20018
Cells. 2020 07 05. pii: E1619. [Epub ahead of print]9(7):

Canonical and Noncanonical Autophagy as Potential Targets for COVID-19.

Melissa Bello-Perez, Isabel Sola, Beatriz Novoa, Daniel J Klionsky, Alberto Falco.

  The SARS-CoV-2 pandemic necessitates a review of the molecular mechanisms underlying cellular infection by coronaviruses, in order to identify potential therapeutic targets against the associated new disease (COVID-19). Previous studies on its counterparts prove a complex and concomitant interaction between coronaviruses and autophagy. The precise manipulation of this pathway allows these viruses to exploit the autophagy molecular machinery while avoiding its protective apoptotic drift and cellular innate immune responses. In turn, the maneuverability margins of such hijacking appear to be so narrow that the modulation of the autophagy, regardless of whether using inducers or inhibitors (many of which are FDA-approved for the treatment of other diseases), is usually detrimental to viral replication, including SARS-CoV-2. Recent discoveries indicate that these interactions stretch into the still poorly explored noncanonical autophagy pathway, which might play a substantial role in coronavirus replication. Still, some potential therapeutic targets within this pathway, such as RAB9 and its interacting proteins, look promising considering current knowledge. Thus, the combinatory treatment of COVID-19 with drugs affecting both canonical and noncanonical autophagy pathways may be a turning point in the fight against this and other viral infections, which may also imply beneficial prospects of long-term protection.

Keywords:  COVID-19; SARS-CoV-2; antiviral; autophagy; canonical autophagy; coronavirus; noncanonical autophagy

DOI:  https://doi.org/10.3390/cells9071619
Exp Neurobiol. 2020 Jun 30. 29(3): 207-218

Death-associated Protein Kinase 1 Phosphorylates α-Synuclein at Ser129 and Exacerbates Rotenone-induced Toxic Aggregation of α-Synuclein in Dopaminergic SH-SY5Y Cells.

Woo Hyun Shin, Kwang Chul Chung.

  The formation of Lewy bodies (LBs), intracellular filamentous inclusions, is one of the hallmarks of Parkinson's disease (PD). α-Synuclein is the main component of LBs and its abnormal accumulation contributes to the pathogenesis of PD. Direct phosphorylation of α-synuclein at multiple Ser/Tyr residues is known to induce its aggregation, consequently promoting LB formation. Death-associated protein kinase 1 (DAPK1), originally identified as a positive mediator of γ-interferon-induced programmed cell death, possesses tumor-suppressive activity and mediates a wide range of cellular processes, including apoptosis and autophagy. Accumulating evidence suggests that DAPK1 is also associated with neuronal cell death and neurodegeneration. For example, DAPK1 phosphorylates tau and amyloid precursor protein, and induces tau aggregation and amyloid β production, respectively, in Alzheimer's disease. DAPK1 is also accumulated to a larger extent in a mouse model of PD, causing synucleinopathy and dopaminergic neuron degeneration. In this study, we attempted to determine whether DAPK1 phosphorylates α-synuclein and affects cell viability in human dopaminergic neuroblastoma SH-SY5Y cells. We demonstrated that DAPK1 directly phosphorylates α-synuclein at Ser129, and induces the formation of insoluble α-synuclein aggregates. We also showed that DAPK1 enhances rotenone-induced aggregation of α-synuclein, potentiating neuronal cell death. Taken together, these findings suggest that DAPK1 acts as a novel regulator of toxic α-synuclein aggregation, possibly affecting and playing a role in the development of PD.

Keywords:  Death-associated protein kinase 1; Parkinson's disease; Phosphorylation; Protein aggregation; α-Synuclein

DOI:  https://doi.org/10.5607/en20014
J Histochem Cytochem. 2020 Jul 06. 22155420937370

Proteoglycan-driven Autophagy: A Nutrient-independent Mechanism to Control Intracellular Catabolism.

Thomas Neill, Simone Buraschi, Aastha Kapoor, Renato V Iozzo.

  Proteoglycans are rapidly emerging as versatile regulators of intracellular catabolic pathways. This is predominantly achieved via the non-canonical induction of autophagy, a fundamentally and evolutionarily conserved eukaryotic pathway necessary for maintaining organismal homeostasis. Autophagy facilitated by either decorin, a small leucine-rich proteoglycan, or perlecan, a basement membrane heparan sulfate proteoglycan, proceeds independently of ambient nutrient conditions. We found that soluble decorin evokes endothelial cell autophagy and breast carcinoma cell mitophagy by directly interacting with vascular endothelial growth factor receptor 2 (VEGFR2) or the Met receptor tyrosine kinase, respectively. Endorepellin, a soluble, proteolytic fragment of perlecan, induces autophagy and endoplasmic reticulum stress within the vasculature, downstream of VEGFR2. These potent matrix-derived cues transduce key biological information via receptor binding to converge upon a newly discovered nexus of core autophagic machinery comprised of Peg3 (paternally expressed gene 3) for autophagy or mitostatin for mitophagy. Here, we give a mechanistic overview of the nutrient-independent, proteoglycan-driven programs utilized for autophagic or mitophagic progression. We propose that catabolic control of cell behavior is an underlying basis for proteoglycan versatility and may provide novel therapeutic targets for the treatment of human disease.

Keywords:  Peg3; autophagy; decorin; endorepellin; extracellular matrix; glycosaminoglycan proteoglycan; mitophagy; mitostatin; perlecan

DOI:  https://doi.org/10.1369/0022155420937370
Mol Cells. 2020 Jul 06.

Lipophagy: Molecular Mechanisms and Implications in Metabolic Disorders.

Dong Wook Shin.

  Autophagy is an intracellular degradation system that breaks down damaged organelles or damaged proteins using intracellular lysosomes. Recent studies have also revealed that various forms of selective autophagy play specific physiological roles under different cellular conditions. Lipid droplets, which are mainly found in adipocytes and hepatocytes, are dynamic organelles that store triglycerides and are critical to health. Lipophagy is a type of selective autophagy that targets lipid droplets and is an essential mechanism for maintaining homeostasis of lipid droplets. However, while processes that regulate lipid droplets such as lipolysis and lipogenesis are relatively well known, the major factors that control lipophagy remain largely unknown. This review introduces the underlying mechanism by which lipophagy is induced and regulated, and the current findings on the major roles of lipophagy in physiological and pathological status. These studies will provide basic insights into the function of lipophagy and may be useful for the development of new therapies for lipophagy dysfunction-related diseases.

Keywords:  adipose; lipid droplets; lipophagy; liver; metabolic disorders; selective autophagy

DOI:  https://doi.org/10.14348/molcells.2020.0046
Biochimie. 2020 Jul 02. pii: S0300-9084(20)30140-1. [Epub ahead of print]

Lipid excess affects chaperone-mediated autophagy in hypothalamus.

M Portovedo, A Reginato, J É Miyamoto, L A Simino, M P Hakim, M Campana, R F Leal, L M Ignácio-Souza, M A Torsoni, C Magnan, H Le Stunff, A S Torsoni, M Milanski.

  Obesity is a major health problem worldwide. Overweight and obesity directly affect health-related quality of life and also have an important economic impact on healthcare systems. In experimental models, obesity leads to hypothalamic inflammation and loss of metabolic homeostasis. It is known that macroautophagy is decreased in the hypothalamus of obese mice but the role of chaperone-mediated autophagy is still unknown. In this study, we aimed to investigate the role of hypothalamic chaperone-mediated autophagy in response to high-fat diet and also the direct effect of palmitate on hypothalamic neurons. Mice received chow or high-fat diet for 3 days or 1 week. At the end of the experimental protocol, chaperone-mediated autophagy in hypothalamus was investigated, as well as cytokines expression. In other set of experiments, neuronal cell lines were treated with palmitic acid, a saturated fatty acid. We show that chaperone-mediated autophagy is differently regulated in response to high-fat diet intake for 3 days or 1 week. Also, when hypothalamic neurons are directly exposed to palmitate there is activation of chaperone-mediated autophagy. High-fat diet causes hypothalamic inflammation concomitantly to changes in the content of chaperone-mediated autophagy machinery. It remains to be studied the direct role of inflammation and lipids itself on the activation of chaperone-mediated autophagy in the hypothalamus in vivo and also the neuronal implications of chaperone-mediated autophagy inhibition in response to obesity.

Keywords:  Autophagy; Chaperone-mediated autophagy; Hypothalamus; Obesity; Palmitic acid

DOI:  https://doi.org/10.1016/j.biochi.2020.06.008
Cell Death Dis. 2020 Jul 08. 11(7): 517

Autophagy as a modulator of cell death machinery.

Masayuki Noguchi, Noriyuki Hirata, Tsutomu Tanaka, Futoshi Suizu, Hiroshi Nakajima, John A Chiorini.

The balance between cell death and survival is a critical parameter in the regulation of cells and the maintenance of homeostasis in vivo. Three major mechanisms for cell death have been identified in mammalian cells: apoptosis (type I), autophagic cell death (type II), and necrosis (type III). These three mechanisms have been suggested to engage in cross talk with each other. Among them, autophagy was originally characterized as a cell survival mechanism for amino acid recycling during starvation. Whether autophagy functions primarily in cell survival or cell death is a critical question yet to be answered. Here, we present a comprehensive review of the cell death-related events that take place during autophagy and their underlying mechanisms in cancer and autoimmune disease development.

DOI: https://doi.org/10.1038/s41419-020-2724-5
J Neurosci Res. 2020 Jul 07.

An update on cellular and molecular determinants of Parkinson's disease with emphasis on the role of the retromer complex.

Vania Macías-Calvio, Luz-María Fuentealba, María-Paz Marzolo.

  Parkinson's disease (PD) is a highly prevalent neurodegenerative condition. The disease involves the progressive degeneration of dopaminergic neurons located in the substantia nigra pars compacta. Among late-onset, familial forms of Parkinson are cases with mutations in the PARK17 locus encoding the vacuolar protein sorting 35 (Vps35), a subunit of the retromer complex. The retromer complex is composed of a heterotrimeric protein core (Vps26-Vps35-Vps29). The best-known role of retromer is the retrieval of cargoes from endosomes to the Golgi complex or the plasma membrane. However, recent literature indicates that retromer performs roles associated with lysosomal and mitochondrial functions and degradative pathways such as autophagy. A common point mutation affecting the retromer subunit Vps35 is D620N, which has been linked to the alterations in the aforementioned cellular processes as well as with neurodegeneration. Here, we review the main aspects of the malfunction of the retromer complex and its implications for PD pathology. Besides, we highlight several controversies still awaiting clarification.

Keywords:  Parkinson's disease; Vps35; autophagy; dopaminergic neuron; lysosomal dysfunction; mitochondria; neurodegeneration; recycling endosome; retromer complex; trans-Golgi network

DOI:  https://doi.org/10.1002/jnr.24675
Cell Mol Neurobiol. 2020 Jul 04.

Parkin, an E3 Ubiquitin Ligase, Plays an Essential Role in Mitochondrial Quality Control in Parkinson's Disease.

Xiao-Le Wang, Si-Tong Feng, Zhen-Zhen Wang, Yu-He Yuan, Nai-Hong Chen, Yi Zhang.

  Parkinson's disease (PD), as one of the complex neurodegenerative disorders, affects millions of aged people. Although the precise pathogenesis remains mostly unknown, a significant number of studies have demonstrated that mitochondrial dysfunction acts as a major role in the pathogeny of PD. Both nuclear and mitochondrial DNA mutations can damage mitochondrial integrity. Especially, mutations in several genes that PD-linked have a closed association with mitochondrial dysfunction (e.g., Parkin, PINK1, DJ-1, alpha-synuclein, and LRRK2). Parkin, whose mutation causes autosomal-recessive juvenile parkinsonism, plays an essential role in mitochondrial quality control of mitochondrial biogenesis, mitochondrial dynamics, and mitophagy. Therefore, we summarized the advanced studies of Parkin's role in mitochondrial quality control and hoped it could be studied further as a therapeutic target for PD.

Keywords:  Mitochondrial biogenesis; Mitochondrial dynamics; Mitophagy; Parkin; Parkinson’s disease

DOI:  https://doi.org/10.1007/s10571-020-00914-2
Inflammation. 2020 Jul 09.

Rapamycin Alleviates Hypertriglyceridemia-Related Acute Pancreatitis via Restoring Autophagy Flux and Inhibiting Endoplasmic Reticulum Stress.

Qixiang Mei, Yue Zeng, Chunlan Huang, Junyuan Zheng, Yuecheng Guo, Junjie Fan, Xinyuan Fu, Xingpeng Wang, Yingying Lu.

  Hypertriglyceridemia (HTG) can aggravate acute pancreatitis (AP), but its pathogenesis remains unclear. As autophagic activity is closely related to lipid metabolism and AP, we investigated the autophagic response in models of AP aggravated by HTG and explored whether rapamycin has a protective effect against HTG-related pancreatitis. HTG-associated AP models were established in vivo in rats and in vitro. The degree of inflammation, pancreatic injury, the expression of endoplasmic reticulum (ER) stress, and autophagy markers (P62, LC3) were compared. Autophagic flux were assessed using immunostaining, electron microscopy, and immunoblotting. Compared with the normal diet group, the high-fat diet (HFD) AP group exhibited more severe pancreatic injury, apoptosis, and blocked autophagic flux. In addition, the three branches (PERK-eIF2α, ATF-6-GRP78, and IRE1-sXBP1) of the unfolded protein response and mTORC1/S6K1 pathway were activated in HFD AP models. Moreover, the same phenomena were confirmed in vitro in palmitic acid-stimulated pancreatic acinar cells. Preincubation with the mTOR inhibitor rapamycin restored the autophagic flux and markedly reduced the adverse effects of HTG. In conclusion, the autophagic flux is impaired in HFD-induced AP models and is strongly associated with ER stress. Rapamycin could prevent the aggravation of HTG-associated AP via inhibiting mTORC1/S6K1 pathway.

Keywords:  acute pancreatitis; autophagy; endoplasmic reticulum stress; hypertriglyceridemia; rapamycin

DOI:  https://doi.org/10.1007/s10753-020-01228-7
Eur J Pharmacol. 2020 Jul 01. pii: S0014-2999(20)30410-6. [Epub ahead of print] 173318

Exogenous supplement of glucagon like peptide-1 protects the heart against aortic banding induced myocardial fibrosis and dysfunction through inhibiting mTOR/p70S6K signaling and promoting autophagy.

Rong-Hua Zheng, Wei-Wei Zhang, Ye-Nan Ji, Xiao-Jie Bai, Cai-Ping Yan, Jin Wang, Feng Bai, Zhi-Qing Zhao.

  Mammalian target of rapamycin (mTOR) and a ribosomal protein S6 kinase (p70S6K) mediate tissue fibrosis and negatively regulate autophagy. This study aims to investigate whether glucagon-like peptide-1 (GLP-1) analog liraglutide protects the heart against aortic banding-induced cardiac fibrosis and dysfunction through inhibiting mTOR/p70S6K signaling and promoting autophagy activity. Male SD rats were randomly divided into four groups (n = 6/each group): sham operated control; abdominal aortic constriction (AAC); liraglutide treatment during AAC (0.3 mg/kg, injected subcutaneously twice daily); rapamycin treatment during AAC (0.2 mg/kg/day, administered by gastric gavage). Relative to the animals with AAC on week 16, liraglutide treatment significantly reduced heart/body weight ratio, inhibited cardiomyocyte hypertrophy, and augmented plasma GLP-1 level and tissue GLP-1 receptor expression. Phosphorylation of mTOR/p70S6K, populations of myofibroblasts and synthesis of collagen I/III in the myocardium were simultaneously inhibited. Furthermore, autophagy regulating proteins: LC3-II/LC3-I ratio and Beclin-1 were upregulated, and p62 was downregulated by liraglutide. Compared with liraglutide group, treatment with rapamycin, a specific inhibitor of mTOR, compatibly augmented GLP-1 receptor level, inhibited phosphorylation of mTOR/p70S6K and expression of p62 as well as increased level of LC3-II/LC3-I ratio and Beclin-1, suggesting that there is an interaction between GLP-1 and mTOR/p70S6K signaling in the regulation of autophagy. In line with these modifications, treatment with liraglutide and rapamycin significantly reduced perivascular/interstitial fibrosis, and preserved systolic/diastolic function. These results suggest that the inhibitory effects of liraglutide on cardiac fibrosis and dysfunction are potentially mediated by inhibiting mTOR/p70S6K signaling and enhancing autophagy activity.

Keywords:  Autophagy; Cardiac fibrosis; Cardiac function; Liraglutide; mTOR/p70S6K

DOI:  https://doi.org/10.1016/j.ejphar.2020.173318
EMBO Rep. 2020 Jul 09. e49583

Lipoic acid rejuvenates aged intestinal stem cells by preventing age-associated endosome reduction.

Gang Du, Yicheng Qiao, Zhangpeng Zhuo, Jiaqi Zhou, Xiaorong Li, Zhiming Liu, Yang Li, Haiyang Chen.

  The age-associated decline of adult stem cell function is closely related to the decline in tissue function and age-related diseases. However, the underlying mechanisms that ultimately lead to the observed functional decline of stem cells still remain largely unexplored. This study investigated Drosophila midguts and found a continuous downregulation of lipoic acid synthase, which encodes the key enzyme for the endogenous synthesis of alpha-lipoic acid (ALA), upon aging. Importantly, orally administration of ALA significantly reversed the age-associated hyperproliferation of intestinal stem cells (ISCs) and the observed decline of intestinal function, thus extending the lifespan of Drosophila. This study reports that ALA reverses age-associated ISC dysfunction by promoting the activation of the endocytosis-autophagy network, which decreases in aged ISCs. Moreover, this study suggests that ALA may be used as a safe and effective anti-aging compound for the treatment of ISC-dysfunction-related diseases and for the promotion of healthy aging in humans.

Keywords:  aging; alpha-lipoic acid; endocytosis; intestinal stem cell; longevity

DOI:  https://doi.org/10.15252/embr.201949583
Proc Natl Acad Sci U S A. 2020 Jul 07. pii: 201922883. [Epub ahead of print]

Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces.

Sai Venkatesh Pingali, Micholas Dean Smith, Shih-Hsien Liu, Takat B Rawal, Yunqiao Pu, Riddhi Shah, Barbara R Evans, Volker S Urban, Brian H Davison, Charles M Cai, Arthur J Ragauskas, Hugh M O'Neill, Jeremy C Smith, Loukas Petridis.

  A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in aqueous solution. Here, neutron scattering and molecular-dynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range (>25 °C) cellulose disruption occurs only above 150 °C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (Rg ∼ 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent water-rich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale.

Keywords:  biomass; pretreatment; solvents

DOI:  https://doi.org/10.1073/pnas.1922883117
Elife. 2020 Jul 10. pii: e57544. [Epub ahead of print]9

Real-time in vivo imaging of extracellular ATP in the brain with a hybrid-type fluorescent sensor.

Nami Kitajima, Kenji Takikawa, Hiroshi Sekiya, Kaname Satoh, Daisuke Asanuma, Hirokazu Sakamoto, Shodai Takahashi, Kenjiro Hanaoka, Yasuteru Urano, Shigeyuki Namiki, Masamitsu Iino, Kenzo Hirose.

  Adenosine 5' triphosphate (ATP) is a ubiquitous extracellular signaling messenger. Here, we describe a method for in-vivo imaging of extracellular ATP with high spatiotemporal resolution. We prepared a comprehensive set of cysteine-substitution mutants of ATP-binding protein, Bacillus FoF1-ATP synthase e subunit, labeled with small-molecule fluorophores at the introduced cysteine residue. Screening revealed that the Cy3-labeled glutamine-105 mutant (Q105C-Cy3; designated ATPOS) shows a large fluorescence change in the presence of ATP, with submicromolar affinity, pH-independence, and high selectivity for ATP over ATP metabolites and other nucleotides. To enable in-vivo validation, we introduced BoNT/C-Hc for binding to neuronal plasma membrane and Alexa Fluor 488 for ratiometric measurement. The resulting ATPOS complex binds to neurons in cerebral cortex of living mice, and clearly visualized a concentrically propagating wave of extracellular ATP release in response to electrical stimulation. ATPOS should be useful to probe the extracellular ATP dynamics of diverse biological processes in vivo.

Keywords:  biochemistry; chemical biology; mouse; neuroscience

DOI:  https://doi.org/10.7554/eLife.57544
Neuroscientist. 2020 Jul 09. 1073858420936162

Mitochondrial Fatty Acids and Neurodegenerative Disorders.

Alexander J Kastaniotis, Kaija J Autio, Remya R Nair.

  Fatty acids in mitochondria, in sensu stricto, arise either as β-oxidation substrates imported via the carnitine shuttle or through de novo synthesis by the mitochondrial fatty acid synthesis (mtFAS) pathway. Defects in mtFAS or processes involved in the generation of the mtFAS product derivative lipoic acid (LA), including iron-sulfur cluster synthesis required for functional LA synthase, have emerged only recently as etiology for neurodegenerative disease. Intriguingly, mtFAS deficiencies very specifically affect CNS function, while LA synthesis and attachment defects have a pleiotropic presentation beyond neurodegeneration. Typical mtFAS defect presentations include optical atrophy, as well as basal ganglia defects associated with dystonia. The phenotype display of patients with mtFAS defects can resemble the presentation of disorders associated with coenzyme A (CoA) synthesis. A recent publication links these processes together based on the requirement of CoA for acyl carrier protein maturation. MtFAS defects, CoA synthesis- as well as Fe-S cluster-deficiencies share lack of LA as a common symptom.

Keywords:  CoA synthesis; CoPAN; MEPAN; PKAN; acyl carrier protein; iron-sulfur cluster synthesis; lipoic acid; mitochondrial fatty acid synthesis; neurodegeneration

DOI:  https://doi.org/10.1177/1073858420936162
Exp Eye Res. 2020 Jul 02. pii: S0014-4835(20)30389-4. [Epub ahead of print] 108131

mTORC1 and mTORC2 expression in inner retinal neurons and glial cells.

Mandy K Losiewicz, Lynda Elghazi, Diane C Fingar, Raju V S Rajala, Stephen I Lentz, Patrice E Fort, Steven F Abcouwer, Thomas W Gardner.

  The retina is one of the most metabolically active tissues, yet the processes that control retinal metabolism remains poorly understood. The mTOR complex (mTORC) that drives protein and lipid biogenesis and autophagy has been studied extensively in regards to retinal development and responses to optic nerve injury but the processes that regulate homeostasis in the adult retina have not been determined. We previously demonstrated that normal adult retina has high rates of protein synthesis compared to skeletal muscle, associated with high levels of mechanistic target of rapamycin (mTOR), a kinase that forms multi-subunit complexes that sense and integrate diverse environmental cues to control cell and tissue physiology. This study was undertaken to: 1) quantify expression of mTOR complex 1 (mTORC1)- and mTORC2-specific partner proteins in normal adult rat retina, brain and liver; and 2) to localize these components in normal human, rat, and mouse retinas. Immunoblotting and immunoprecipitation studies revealed greater expression of raptor (exclusive to mTORC1) and rictor (exclusive for mTORC2) in normal rat retina relative to liver or brain, as well as the activating mTORC components, pSIN1 and pPRAS40. By contrast, liver exhibits greater amounts of the mTORC inhibitor, DEPTOR. Immunolocalization studies for all three species showed that mTOR, raptor, and rictor, as well as most other known components of mTORC1 and mTORC2, were primarily localized in the inner retina with mTORC1 primarily in retinal ganglion cells (RGCs) and mTORC2 primarily in glial cells. In addition, phosphorylated ribosomal protein S6, a direct target of the mTORC1 substrate ribosomal protein S6 kinase beta-1 (S6K1), was readily detectable in RGCs, indicating active mTORC1 signaling, and was preserved in human donor eyes. Collectively, this study demonstrates that the inner retina expresses high levels of mTORC1 and mTORC2 and possesses active mTORC1 signaling that may provide cell- and tissue-specific regulation of homeostatic activity. These findings help to define the physiology of the inner retina, which is key for understanding the pathophysiology of optic neuropathies, glaucoma and diabetic retinopathy.

Keywords:  Protein synthesis; Raptor; Retina; Retinal ganglion cells; Rictor; mTORC

DOI:  https://doi.org/10.1016/j.exer.2020.108131
Proc Natl Acad Sci U S A. 2020 Jul 06. pii: 201922184. [Epub ahead of print]

Dopaminergic neurodegeneration induced by Parkinson's disease-linked G2019S LRRK2 is dependent on kinase and GTPase activity.

An Phu Tran Nguyen, Elpida Tsika, Kaela Kelly, Nathan Levine, Xi Chen, Andrew B West, Sylviane Boularand, Pascal Barneoud, Darren J Moore.

  Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of late-onset, autosomal-dominant familial Parkinson's disease (PD). LRRK2 functions as both a kinase and GTPase, and PD-linked mutations are known to influence both enzymatic activities. While PD-linked LRRK2 mutations can commonly induce neuronal damage in culture models, the mechanisms underlying these pathogenic effects remain uncertain. Rodent models containing familial LRRK2 mutations often lack robust PD-like neurodegenerative phenotypes. Here, we develop a robust preclinical model of PD in adult rats induced by the brain delivery of recombinant adenoviral vectors with neuronal-specific expression of human LRRK2 harboring the most common G2019S mutation. In this model, G2019S LRRK2 induces the robust degeneration of substantia nigra dopaminergic neurons, a pathological hallmark of PD. Introduction of a stable kinase-inactive mutation or administration of the selective kinase inhibitor, PF-360, attenuates neurodegeneration induced by G2019S LRRK2. Neuroprotection provided by pharmacological kinase inhibition is mediated by an unusual mechanism involving the robust destabilization of human LRRK2 protein in the brain relative to endogenous LRRK2. Our study further demonstrates that G2019S LRRK2-induced dopaminergic neurodegeneration critically requires normal GTPase activity, as hypothesis-testing mutations that increase GTP hydrolysis or impair GTP-binding activity provide neuroprotection although via distinct mechanisms. Taken together, our data demonstrate that G2019S LRRK2 induces neurodegeneration in vivo via a mechanism that is dependent on kinase and GTPase activity. Our study provides a robust rodent preclinical model of LRRK2-linked PD and nominates kinase inhibition and modulation of GTPase activity as promising disease-modifying therapeutic targets.

Keywords:  GTPase; LRRK2; Rab; kinase; neurodegeneration

DOI:  https://doi.org/10.1073/pnas.1922184117
Genes (Basel). 2020 Jul 02. pii: E738. [Epub ahead of print]11(7):

Experimental Approaches in Delineating mTOR Signaling.

Jiayi Qian, Siyuan Su, Pengda Liu.

  The mTOR signaling controls essential biological functions including proliferation, growth, metabolism, autophagy, ageing, and others. Hyperactivation of mTOR signaling leads to a plethora of human disorders; thus, mTOR is an attractive drug target. The discovery of mTOR signaling started from isolation of rapamycin in 1975 and cloning of TOR genes in 1993. In the past 27 years, numerous research groups have contributed significantly to advancing our understanding of mTOR signaling and mTOR biology. Notably, a variety of experimental approaches have been employed in these studies to identify key mTOR pathway members that shape up the mTOR signaling we know today. Technique development drives mTOR research, while canonical biochemical and yeast genetics lay the foundation for mTOR studies. Here in this review, we summarize major experimental approaches used in the past in delineating mTOR signaling, including biochemical immunoprecipitation approaches, genetic approaches, immunofluorescence microscopic approaches, hypothesis-driven studies, protein sequence or motif search driven approaches, and bioinformatic approaches. We hope that revisiting these distinct types of experimental approaches will provide a blueprint for major techniques driving mTOR research. More importantly, we hope that thinking and reasonings behind these experimental designs will inspire future mTOR research as well as studies of other protein kinases beyond mTOR.

Keywords:  biochemical approach; bioinformatic approach; experimental approach; genetic approach; hypothesis-driven; immunofluorescence; mTOR; protein motif search

DOI:  https://doi.org/10.3390/genes11070738
Cancer Lett. 2020 Jul 04. pii: S0304-3835(20)30346-3. [Epub ahead of print]

Autophagy in the crosstalk between tumor and microenvironment.

Olivier Camuzard, Sabine Santucci-Darmanin, Georges F Carle, Valérie Pierrefite-Carle.

  Autophagy is the major catabolic process in eukaryotic cells for the degradation and recycling of damaged macromolecules and organelles. It plays a crucial role in cell quality control and nutrient supply under stress conditions. Although autophagy is classically described as a degradative mechanism, it can also be involved in some secretion pathways, leading to the extracellular release of proteins, aggregates, or organelles. The role of autophagy in cancer is complex and depends on tumor development stage. While autophagy limits cancer development in the early stages of tumorigenesis, it can also have a protumoral role in more advanced cancers, promoting primary tumor growth and metastatic spread. In addition to its pro-survival role in established tumors, autophagy recently emerged as an active player in the crosstalk between tumor and stromal cells. The aim of this review is to analyze the impact of tumoral autophagy on the microenvironment and conversely the effect of stromal cell autophagy on tumor cells.

Keywords:  Autophagosome; Cancer; Degradation; Secretion; Stromal cells

DOI:  https://doi.org/10.1016/j.canlet.2020.06.015
Mol Med Rep. 2020 Aug;22(2): 1295-1302

Overexpression of ATG4a promotes autophagy and proliferation, and inhibits apoptosis in lens epithelial cells via the AMPK and Akt pathways.

Chufan Yan, Jiangyue Zhao, Yu Qin, Fangkun Zhao, Liyang Ji, Jinsong Zhang.

Autophagy is a major intracellular degradation system that plays an important role in several biological processes. Although some studies indicate that autophagy may play a role in lens degradation and cataracts formation, its underlying mechanism remains to be elucidated. Autophagy‑related gene 4a (ATG4a) cleaves autophagy‑related protein 8 (Atg8) near the C terminus, allowing Atg8 to conjugate with phosphatidylethanolamine via the exposed glycine; although this is pivotal in cancer development, no study has yet linked it to eye diseases. In the present study, the protein expression of ATG4a is significantly upregulated in hydrogen peroxide‑treated lens epithelial cells (HLE‑B3), indicating that ATG4a may play an important role in lens degradation. ATG4a was overexpressed using lentivirus in lens epithelial cells to observe the effect of ATG4a on various phenotypes by transmission electron microscopy, western blotting, EdU incorporation assay, flow cytometry and in situ cell death detection. The results demonstrated that the overexpression of ATG4a could promote autophagy by promoting the adenosine 5'‑monophosphate‑activated protein kinase pathway and inhibiting the Akt pathway. It also upregulated the proliferation and downregulated the apoptosis of lens epithelial cells. Overall, the present study showed that ATG4a plays a vital role in lens degradation and that it could be a potential target in cataract therapies.

DOI: https://doi.org/10.3892/mmr.2020.11205
Mech Ageing Dev. 2020 Jul 01. pii: S0047-6374(20)30092-0. [Epub ahead of print] 111296

ATM-deficient neural precursors develop senescence phenotype with disturbances in autophagy.

Piotr Sunderland, Justyna Augustyniak, Jacek Lenart, Leonora Bużańska, Luigi Carlessi, Domenico Delia, Ewa Sikora.

  ATM is a kinase involved in DNA damage response (DDR), regulation of response to oxidative stress, autophagy and mitophagy. Mutations in the ATM gene in humans result in ataxi A-Telangiectasia disease (A-T) characterized by a variety of symptoms with neurodegeneration and premature ageing among them. Since brain is one of the most affected organs in A-T, we have focused on senescence of neural progenitor cells (NPCs) derived from A-T reprogrammed fibroblasts. Accordingly, A-T NPCs obtained through neural differentiation of iPSCs in 5% oxygen possessed some features of senescence including increased activity of SA-β-gal and secretion of IL6 and IL8 in comparison to control NPCs. This phenotype of A-T NPC was accompanied by elevated oxidative stress. A-T NPCs exhibited symptoms of impaired autophagy and mitophagy with lack of response to chloroquine treatment. Additional sources of oxidative stress like increased oxygen concentration (20 %) and H2O2 respectively aggravated the phenotype of senescence and additionally disturbed the process of mitophagy. In both cases only A-T NPCs reacted to the treatment. We conclude that oxidative stress may be responsible for the phenotype of senescence and impairment of autophagy in A-T NPCs. Our results point to senescent A-T cells as a potential therapeutic target in this disease.

Keywords:  ATM; Ataxia-telangiectasia; Autophagy; Mitophagy; Neural progenitors; Oxidative stress; Senescence; hiPSCs

DOI:  https://doi.org/10.1016/j.mad.2020.111296
Trends Biochem Sci. 2020 Jul 02. pii: S0968-0004(20)30151-1. [Epub ahead of print]

Molecular Mechanisms of Lysosome and Nucleus Communication.

Qian Zhao, Shihong Max Gao, Meng C Wang.

  Lysosomes transcend the role of degradation stations, acting as key nodes for interorganelle crosstalk and signal transduction. Lysosomes communicate with the nucleus through physical proximity and functional interaction. In response to external and internal stimuli, lysosomes actively adjust their distribution between peripheral and perinuclear regions and modulate lysosome-nucleus signaling pathways; in turn, the nucleus fine-tunes lysosomal biogenesis and functions through transcriptional controls. Changes in coordination between these two essential organelles are associated with metabolic disorders, neurodegenerative diseases, and aging. In this review, we address recent advances in lysosome-nucleus communication by multi-tiered regulatory mechanisms and discuss how these regulations couple metabolic inputs with organellar motility, cellular signaling, and transcriptional network.

Keywords:  lysosomal adaptation; lysosomal metabolites; lysosome positioning; lysosome-to-nucleus signaling; transcription factors

DOI:  https://doi.org/10.1016/j.tibs.2020.06.004
Clin Exp Ophthalmol. 2020 Jul 08.

Metabolic pathways in context: mTOR signalling in the retina and optic nerve.

Anthony Yao, Peter van Wijngaarden.

  The mechanistic target of rapamycin (mTOR) signalling network plays a key role in growth and development, autophagy, metabolism, inflammation as well as ageing, and it is therefore important in ocular health and disease. mTOR dysregulation has been identified in a range of conditions, including age-related macular degeneration, diabetic retinopathy, retinitis pigmentosa, traumatic optic neuropathy and glaucoma. Experimental modulation of the pathway has contributed to the understanding of these diseases and offers the potential for new avenues of therapy. This review discusses the mTOR pathway and its role in health and in diseases of the retina and optic nerve. This article is protected by copyright. All rights reserved.

Keywords:  Metabolism; Optic nerve; Retina; mTOR

DOI:  https://doi.org/10.1111/ceo.13819